This dataset contains chromatographic and mass spectrometry (HPLC-MS) data derived from crude organic extracts of Rhizopus microsporus strains cultured under laboratory conditions. The aim of the analysis was to detect and quantify rhizoxin-related compounds, a group of secondary metabolites with known cytotoxic and phytotoxic activities. Extracts were obtained from both wild-type (ATCC 11559) and endobacteria-harboring (infected) or cured strains of R. microsporus (ATCC 52814), following a standardized extraction protocol using ethyl acetate and methanol resuspension. Chromatograms were acquired using HPLC with UV detection at 310 nm, and molecular ions were analyzed via high-resolution mass spectrometry (HR-MS).